Contacts of the helix formed by residues 1204 - 1213 (chain A) in PDB entry 4M76
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY1204 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1203A LYS* 1.3 74.2 - - - +
1205A PRO* 1.3 70.4 - - - +
1207A LEU* 3.2 18.7 + - - +
1208A ASN* 3.2 12.5 + - - +
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Residues in contact with PRO1205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1181A MET* 3.5 25.5 - - + +
1203A LYS 3.7 2.9 - - - +
1204A GLY* 1.3 82.6 - - - +
1206A LEU* 1.3 66.1 + - + +
1208A ASN* 3.8 8.0 - - + +
1209A LYS* 2.9 30.5 + - - +
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Residues in contact with LEU1206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1177A GLU* 3.6 35.4 - - + +
1180A TYR* 3.4 37.8 - - + -
1181A MET* 3.7 27.4 - - + -
1196A LEU* 4.2 10.5 - - + -
1201A ARG 3.4 23.1 - - - +
1202A LEU* 3.8 14.0 - - + +
1203A LYS 3.4 11.2 - - - +
1204A GLY 3.2 0.4 - - - -
1205A PRO* 1.3 81.4 - - + +
1207A LEU* 1.3 58.3 + - - +
1209A LYS* 3.5 0.3 - - - +
1210A PHE* 3.1 23.2 + - - +
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Residues in contact with LEU1207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1202A LEU* 4.0 26.4 - - + +
1203A LYS* 3.6 6.5 + - - -
1204A GLY 3.2 14.4 + - - +
1206A LEU* 1.3 76.4 - - - +
1208A ASN* 1.3 61.4 + - - +
1210A PHE* 3.0 7.6 + - + +
1211A LEU* 2.9 56.8 + - + +
1243A LEU* 3.7 29.8 - - + -
208B ARG* 3.7 27.1 - - - +
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Residues in contact with ASN1208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1204A GLY 3.2 9.5 + - - +
1205A PRO* 3.8 10.7 - - + +
1206A LEU 3.4 0.2 - - - -
1207A LEU* 1.3 80.5 - - - +
1209A LYS* 1.3 55.6 + - - +
1211A LEU* 4.8 5.8 - - - -
1212A THR* 2.4 55.7 + - - +
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Residues in contact with LYS1209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1180A TYR* 3.7 33.4 - - + +
1181A MET* 3.5 34.0 + - + +
1183A LEU 2.5 30.4 + - - -
1184A GLN* 4.9 3.6 + - - +
1189A VAL* 4.1 16.2 - - + -
1205A PRO 2.9 19.1 + - - +
1206A LEU 3.5 4.7 - - - +
1208A ASN* 1.3 77.6 + - - +
1210A PHE* 1.3 57.3 + - - +
1212A THR* 3.5 5.3 + - - +
1213A THR* 2.3 41.0 + - - +
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Residues in contact with PHE1210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1180A TYR* 3.4 19.3 - - - +
1189A VAL* 3.6 19.3 - - + -
1190A ALA* 4.0 18.2 - - - -
1193A GLY* 4.3 5.4 - - - -
1202A LEU* 4.4 14.8 - - + -
1206A LEU 3.1 13.8 + - - +
1207A LEU* 3.0 13.1 + - + +
1209A LYS* 1.3 80.3 - - - +
1211A LEU* 1.3 74.5 + - + +
1213A THR* 3.5 3.1 + - - -
1220A TRP* 3.1 46.1 + + - -
1236A ALA* 3.6 31.0 - - + -
1239A ALA* 3.7 17.7 - - + -
1240A LEU* 3.9 22.2 - - + -
1243A LEU* 5.3 0.7 - - + -
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Residues in contact with LEU1211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1207A LEU* 2.9 45.6 + - + +
1208A ASN* 4.3 5.8 - - - +
1210A PHE* 1.3 89.6 - - + +
1212A THR* 1.3 63.8 + - + +
1214A ALA* 3.4 21.1 + - - +
1217A LYS* 5.4 2.3 - - - +
1220A TRP* 4.5 3.1 - - + -
1240A LEU* 4.0 21.1 - - + -
1245A ASP* 4.4 2.2 - - - +
1248A PHE* 4.2 39.4 - - + -
178B GLU* 5.2 4.3 - - - +
208B ARG* 4.1 21.1 - - - +
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Residues in contact with THR1212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1208A ASN* 2.4 48.1 + - - +
1209A LYS* 3.5 6.6 + - - -
1211A LEU* 1.3 77.6 - - + +
1213A THR* 1.3 64.4 + - - +
1214A ALA 3.2 7.9 + - - +
178B GLU* 6.0 1.6 - - - +
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Residues in contact with THR1213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1184A GLN 5.6 2.9 - - - +
1185A ARG 5.3 0.4 - - - -
1186A SER* 3.4 39.2 + - - +
1189A VAL* 3.6 24.2 - - + +
1209A LYS* 2.3 33.6 + - - +
1210A PHE 3.7 7.6 - - - -
1211A LEU 3.2 0.8 - - - -
1212A THR* 1.3 76.8 - - - +
1214A ALA* 1.3 64.7 - - - +
1215A LYS* 3.3 3.8 + - - +
1219A ARG 4.7 0.2 - - - +
1220A TRP* 4.0 7.6 - - + -
1221A GLU 5.2 0.7 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il